Merge pull request #405 from tgen/develop

Mutation burden bugfix
tgen · Feb 9, 2021 · c99cc7c · c99cc7c
2 parents 436aae1 + 08097ad
commit c99cc7c
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/modules/metrics/main.jst b/modules/metrics/main.jst
@@ -42,7 +42,12 @@
 
 {% if tasks[taskPrefix+"_somatic_sample_metric_tgen_mutation_burden"]|default(true) %}
   {% if flags.bcftools %}
-    {% set final_vcf_prefix %}{{ vcf_prefix }}.db{% endset %}
+    {# If pair.normal.pathToBam is defined then we have a tumor_only pair #}
+    {% if pair.normal.pathToBam is defined %}
+      {% set final_vcf_prefix %}{{ vcf_prefix }}.db.flt{% endset %}
+    {% else %}
+      {% set final_vcf_prefix %}{{ vcf_prefix }}.db{% endset %}
+    {% endif %}
   {% else %}
     {% set final_vcf_prefix %}{{ vcf_prefix }}{% endset %}
   {% endif %}
@@ -60,4 +65,4 @@
   {{- msisensor_pro(pair, normal_bam, tumor_bam, aligner) }}
 {% endif %}
 
-{% endmacro %}
+{% endmacro %}